|
| Status |
Public on May 08, 2024 |
| Title |
YUPEET_3 |
| Sample type |
SRA |
| |
|
| Source name |
Primary melanoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
age at diagnosis: 54
cohort: Yale
cell type: Primary melanoma cells
|
| Growth protocol |
Primary melanocytes were grown in melanocyte growth media. WM35, 983, 902, and 1552 cell lines were grown in 2% tumor media. YUPEET and YUCHIME cell lines were grown in basic FGF media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted and RNA was harvested using the Qiagen Rneasy kit. Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero (for removal of rRNA) (Cat#20020598) was used with 1.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned and counts called using STAR.
DEseq2 was used to normalize expression counts and perform DEG analysis.
GSEA was performed for each comparison against all HALLMARK and Curated-Canonical pathways from the MSigDB.
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
May 08, 2024 |
| Contact name |
Tiphaine Christiane Martin |
| E-mail(s) |
tiphaine.martin@mssm.edu
|
| Phone |
2128248403
|
| Organization name |
Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute
|
| Department |
Oncological Sciences
|
| Lab |
Parsons
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
75459 |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE198425 |
Next Generation Sequencing of Primary Melanocytes, Epgn1, and Epgn3 Melanoma Cell lines [RNA-seq] |
| GSE198432 |
An epigenetic gene signature underlies phenotype switching in early stage melanomas. |
|
| Relations |
| BioSample |
SAMN26581348 |
| SRA |
SRX14438463 |
